Switch spectral format from MGF to mzML

[ypriverol]

Summary

Update ThermoRawFileParser to output mzML (-f=2), adapt xiSEARCH module to accept mzML input, adapt mass recalibration script (recalibrate_mgf.py -> recalibrate_spectra.py) to read/write mzML via pyopenms, remove FORMAT_CORRECTION step (MGF-specific). Both xiSEARCH and Scout support mzML natively.

Motivation

Standardize on mzML as the intermediate spectral format. This enables both xiSEARCH and Scout to share the same conversion step.

Tasks

• Change ThermoRawFileParser -f=0 (MGF) to -f=2 (mzML) in modules.config
• Update xiSEARCH module to accept mzML
• Adapt recalibrate_mgf.py for mzML I/O (rename to recalibrate_spectra.py)
• Remove FORMAT_CORRECTION step from workflow
• Update all channel variable names (ch_mgf -> ch_mzml)